SMTL ID : 7lmz.1

Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

1 x UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK- UNK: Hexa-ubiquitin(Non-covalent)

UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK.1: 23 residues within 4Å: Chain A: M.550, W.551, F.552 Chain B: M.550, W.551, F.552, G.593 Chain C: M.550, W.551, F.552, G.591, G.593 Chain D: M.550, W.551, F.552, D.592, G.593 Chain E: M.550, W.551, F.552, D.592, G.593, G.594 18 PLIP interactions: 5 interactions with chain E, 4 interactions with chain B, 4 interactions with chain D, 1 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: E:W.551, E:D.592, B:W.551, D:W.551 Hydrogen bonds: E:M.550, E:G.593, E:G.594, B:M.550, B:F.552, B:G.593, D:M.550, D:F.552, D:G.593, A:F.552, C:M.550, C:F.552, C:G.591, C:G.593

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 14 residues within 4Å: Chain A: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685, T.688 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:L.526, A:T.688 Salt bridges: A:K.524 ADP.3: 16 residues within 4Å: Chain A: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409 Chain F: R.359, F.360 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:G.250, A:K.251 Salt bridges: A:K.251, A:K.251, F:R.359 ADP.5: 14 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, A.409, A.412 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.207, B:G.207, B:G.248, B:T.249, B:G.250, B:K.251, B:T.252, B:L.253 Salt bridges: B:K.251 ADP.20: 14 residues within 4Å: Chain F: I.479, G.480, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, A.685, T.688 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.480, F:G.480, F:P.519, F:G.521, F:C.522, F:G.523, F:K.524, F:T.525, F:T.525, F:L.526, F:T.688 Salt bridges: F:K.524

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 22 residues within 4Å: Chain A: D.609, R.635, R.638 Chain B: D.478, I.479, G.480, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.6 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.480, B:P.519, B:G.521, B:C.522, B:C.522, B:G.523, B:K.524, B:T.525, B:L.526, B:Q.578, B:N.624, B:N.624, B:T.688, A:R.635 Salt bridges: B:K.524, B:K.524, A:R.635, A:R.635, A:R.635, A:R.638 ATP.7: 23 residues within 4Å: Chain B: D.333, R.359, R.362 Chain C: D.205, I.206, G.207, C.209, P.246, P.247, G.248, T.249, G.250, K.251, T.252, L.253, R.256, E.305, N.348, I.380, H.384, G.408, A.409 Ligands: MG.9 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:L.253, C:R.256, C:R.256, C:N.348 Salt bridges: C:K.251, C:K.251, B:R.359, B:R.359, B:R.359, B:R.362 ATP.8: 21 residues within 4Å: Chain B: D.609, R.635, R.638 Chain C: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.10 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:G.523, C:K.524, C:T.525, C:L.526, C:Q.578, C:N.624, C:N.624, C:T.688 Salt bridges: C:K.524, C:K.524, B:R.635, B:R.635, B:R.635, B:R.638 ATP.11: 21 residues within 4Å: Chain C: D.333, R.359, R.362 Chain D: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, R.256, E.305, N.348, I.380, H.384, G.408, A.409 Ligands: MG.13 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.207, D:G.248, D:T.249, D:T.249, D:T.249, D:G.250, D:K.251, D:T.252, D:L.253, D:N.348, D:N.348 Salt bridges: D:K.251, D:K.251, D:R.256, C:R.359, C:R.359, C:R.359, C:R.362 ATP.12: 22 residues within 4Å: Chain C: D.609, R.635, R.638 Chain D: D.478, I.479, G.480, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.14 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.480, D:G.480, D:P.519, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:L.526, D:Q.578, D:N.624, D:T.688 Salt bridges: D:K.524, D:K.524, C:R.635, C:R.635, C:R.635, C:R.638 ATP.15: 21 residues within 4Å: Chain D: D.333, R.359, R.362 Chain E: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, R.256, E.305, N.348, I.380, H.384, G.408, A.409 Ligands: MG.17 20 PLIP interactions: 16 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:L.253, E:R.256, E:E.305, E:N.348 Salt bridges: E:K.251, E:K.251, E:R.256, D:R.359, D:R.359, D:R.359, D:R.362 ATP.16: 21 residues within 4Å: Chain D: D.609, R.635, R.638 Chain E: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.18 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:C.522, E:G.523, E:K.524, E:T.525, E:L.526, E:Q.578, E:N.624, E:T.688 Salt bridges: E:K.524, E:K.524, D:R.635, D:R.635, D:R.635, D:R.638 ATP.19: 16 residues within 4Å: Chain F: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.21 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.207, F:G.248, F:T.249, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:L.253, F:N.348 Salt bridges: F:K.251, F:K.251

8 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.609, R.638 Chain B: T.525 Ligands: ATP.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:T.525, A:D.609 MG.9: 3 residues within 4Å: Chain C: T.252, D.304 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.252 MG.10: 6 residues within 4Å: Chain B: D.609, R.638 Chain C: T.525, D.577, Q.578 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.525 MG.13: 4 residues within 4Å: Chain D: T.252, D.304, E.305 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.252 MG.14: 6 residues within 4Å: Chain C: D.609, R.638 Chain D: T.525, D.577, Q.578 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.525 MG.17: 3 residues within 4Å: Chain E: T.252, D.304 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.252 MG.18: 5 residues within 4Å: Chain D: R.638 Chain E: T.525, D.577, Q.578 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.525 MG.21: 3 residues within 4Å: Chain F: T.252, D.304 Ligands: ATP.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, M. et al., Mechanistic insight into substrate processing and allosteric inhibition of human p97. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-09-15

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Transitional endoplasmic reticulum ATPase

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